Zinc in PDB 8uw6: Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.

Enzymatic activity of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.

All present enzymatic activity of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.:
3.5.1.16;

Protein crystallography data

The structure of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form., PDB code: 8uw6 was solved by J.Osipiuk, M.Endres, E.Kelley, D.P.Becker, A.Joachimiak, Center Forstructural Biology Of Infectious Diseases (Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.399, 126.323, 123.408, 90, 90.88, 90
R / Rfree (%) 16.3 / 20.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. (pdb code 8uw6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form., PDB code: 8uw6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8uw6

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Zinc binding site 1 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:13.8
occ:1.00
 OD1 A:ASP112 1.9 14.4 1.0
NE2 A:HIS80 2.0 10.9 1.0
O2 A:TRS505 2.0 12.1 0.8
OE1 A:GLU169 2.0 14.6 1.0
CD A:GLU169 2.7 14.6 1.0
OE2 A:GLU169 2.8 14.8 1.0
C2 A:TRS505 2.9 14.3 0.8
CE1 A:HIS80 3.0 11.2 1.0
CG A:ASP112 3.0 14.2 1.0
CD2 A:HIS80 3.0 11.4 1.0
OD2 A:ASP112 3.3 14.7 1.0
ZN A:ZN502 3.4 17.1 0.8
OE1 A:GLU144 3.5 16.6 1.0
C1 A:TRS505 3.6 16.1 0.8
OE2 A:GLU145 3.7 17.6 1.0
C A:TRS505 3.7 15.9 0.8
O1 A:TRS505 3.9 18.7 0.8
ND1 A:HIS80 4.1 11.5 1.0
CD A:GLU144 4.1 16.5 1.0
CG A:HIS80 4.2 11.3 1.0
CG A:GLU169 4.2 13.6 1.0
CG A:MET113 4.3 12.8 1.0
CB A:ASP112 4.3 13.1 1.0
CD A:GLU145 4.3 18.3 1.0
N A:TRS505 4.4 17.8 0.8
SD A:MET113 4.5 12.7 1.0
OE2 A:GLU144 4.5 18.0 1.0
CB A:MET113 4.6 13.0 1.0
CA A:ASP112 4.7 12.8 1.0
CD A:PRO170 4.7 11.7 1.0
C A:ASP112 4.7 12.9 1.0
OE1 A:GLU145 4.7 17.9 1.0
CB A:GLU169 4.8 13.1 1.0
O A:ASP112 4.9 12.3 1.0
N A:MET113 5.0 12.7 1.0

Zinc binding site 2 out of 10 in 8uw6

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Zinc binding site 2 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:17.1
occ:0.80
 OE2 A:GLU145 2.1 17.6 1.0
NE2 A:HIS355 2.1 16.5 1.0
O2 A:TRS505 2.1 12.1 0.8
OD2 A:ASP112 2.1 14.7 1.0
N A:TRS505 2.2 17.8 0.8
OE1 A:GLU145 2.5 17.9 1.0
CD A:GLU145 2.6 18.3 1.0
CE1 A:HIS355 2.9 20.4 1.0
C2 A:TRS505 3.0 14.3 0.8
C A:TRS505 3.0 15.9 0.8
CG A:ASP112 3.1 14.2 1.0
CD2 A:HIS355 3.2 17.3 1.0
ZN A:ZN501 3.4 13.8 1.0
OD1 A:ASP112 3.4 14.4 1.0
C1 A:TRS505 3.4 16.1 0.8
OE1 A:GLU144 4.0 16.6 1.0
CG A:GLU145 4.1 17.0 1.0
O A:HOH915 4.1 37.1 1.0
O A:HOH753 4.1 13.8 1.0
ND1 A:HIS355 4.2 18.2 1.0
CG A:HIS355 4.3 18.8 1.0
C3 A:TRS505 4.4 18.6 0.8
CB A:ASP112 4.4 13.1 1.0
NE2 A:HIS80 4.5 10.9 1.0
O A:HOH828 4.6 31.3 1.0
CE1 A:HIS80 4.7 11.2 1.0
O A:HOH768 4.7 29.9 1.0
O1 A:TRS505 4.7 18.7 0.8
O3 A:TRS505 4.7 18.9 0.8
CG1 A:VAL84 4.8 18.2 1.0
OE1 A:GLU169 4.9 14.6 1.0

Zinc binding site 3 out of 10 in 8uw6

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Zinc binding site 3 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:18.5
occ:1.00
 O2 B:TRS504 1.9 17.1 0.8
OD1 B:ASP112 1.9 19.1 1.0
OE1 B:GLU169 2.0 17.9 1.0
NE2 B:HIS80 2.1 17.6 1.0
CD B:GLU169 2.6 15.5 1.0
OE2 B:GLU169 2.7 15.7 1.0
C2 B:TRS504 2.9 21.1 0.8
CG B:ASP112 2.9 18.9 1.0
CE1 B:HIS80 3.0 17.3 1.0
CD2 B:HIS80 3.1 15.9 1.0
OD2 B:ASP112 3.3 19.8 1.0
ZN B:ZN502 3.4 22.2 0.8
OE1 B:GLU144 3.5 20.7 1.0
C3 B:TRS504 3.6 24.4 0.8
OE2 B:GLU145 3.7 22.5 1.0
C B:TRS504 3.8 24.1 0.8
O3 B:TRS504 3.8 25.8 0.8
CG B:GLU169 4.1 15.8 1.0
ND1 B:HIS80 4.2 16.3 1.0
CD B:GLU144 4.2 21.0 1.0
CG B:HIS80 4.2 15.8 1.0
CB B:ASP112 4.3 18.6 1.0
CG B:MET113 4.3 17.0 1.0
CD B:GLU145 4.4 20.4 1.0
N B:TRS504 4.4 22.7 0.8
SD B:MET113 4.5 16.6 1.0
CB B:MET113 4.5 16.2 1.0
CD B:PRO170 4.6 18.3 1.0
CA B:ASP112 4.7 17.9 1.0
C B:ASP112 4.7 17.8 1.0
OE2 B:GLU144 4.7 23.8 1.0
OE1 B:GLU145 4.7 20.4 1.0
CB B:GLU169 4.7 16.1 1.0
O B:ASP112 4.9 17.4 1.0
N B:MET113 5.0 17.1 1.0

Zinc binding site 4 out of 10 in 8uw6

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Zinc binding site 4 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:22.2
occ:0.80
 NE2 B:HIS355 2.1 19.1 1.0
OD2 B:ASP112 2.1 19.8 1.0
OE2 B:GLU145 2.1 22.5 1.0
O2 B:TRS504 2.1 17.1 0.8
N B:TRS504 2.2 22.7 0.8
OE1 B:GLU145 2.5 20.4 1.0
CD B:GLU145 2.6 20.4 1.0
C B:TRS504 2.9 24.1 0.8
C2 B:TRS504 2.9 21.1 0.8
CE1 B:HIS355 3.0 23.7 1.0
CD2 B:HIS355 3.1 22.2 1.0
CG B:ASP112 3.2 18.9 1.0
C3 B:TRS504 3.3 24.4 0.8
ZN B:ZN501 3.4 18.5 1.0
OD1 B:ASP112 3.6 19.1 1.0
OE1 B:GLU144 4.1 20.7 1.0
O B:HOH683 4.1 17.5 1.0
CG B:GLU145 4.1 20.0 1.0
ND1 B:HIS355 4.2 22.6 1.0
CG B:HIS355 4.2 22.3 1.0
C1 B:TRS504 4.4 25.4 0.8
CB B:ASP112 4.5 18.6 1.0
O B:HOH780 4.5 37.7 1.0
O3 B:TRS504 4.6 25.8 0.8
NE2 B:HIS80 4.6 17.6 1.0
O B:HOH665 4.7 32.4 1.0
O1 B:TRS504 4.7 27.1 0.8
CE1 B:HIS80 4.8 17.3 1.0
CG1 B:VAL84 4.8 22.5 1.0
OE1 B:GLU169 4.8 17.9 1.0
CB B:ALA354 4.9 23.5 1.0

Zinc binding site 5 out of 10 in 8uw6

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Zinc binding site 5 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:21.5
occ:0.90
 NE2 B:HIS383 2.0 37.3 1.0
NE2 B:HIS378 2.1 24.4 1.0
CD2 B:HIS378 3.0 25.3 1.0
CD2 B:HIS383 3.0 37.6 1.0
CE1 B:HIS383 3.1 36.5 1.0
CE1 B:HIS378 3.1 25.8 1.0
CG B:HIS383 4.1 37.6 1.0
ND1 B:HIS383 4.1 34.6 1.0
CG B:HIS378 4.2 22.3 1.0
ND1 B:HIS378 4.2 25.4 1.0

Zinc binding site 6 out of 10 in 8uw6

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Zinc binding site 6 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:14.3
occ:1.00
 OD1 C:ASP112 1.9 16.3 1.0
OE1 C:GLU169 2.0 13.1 1.0
NE2 C:HIS80 2.0 11.6 1.0
O2 C:TRS504 2.1 12.6 0.9
CD C:GLU169 2.7 14.1 1.0
OE2 C:GLU169 2.8 14.2 1.0
C2 C:TRS504 2.8 16.0 0.9
CE1 C:HIS80 2.9 12.1 1.0
CG C:ASP112 2.9 15.0 1.0
CD2 C:HIS80 3.0 12.0 1.0
OD2 C:ASP112 3.3 15.9 1.0
ZN C:ZN502 3.4 19.6 0.8
OE1 C:GLU144 3.6 18.0 1.0
C1 C:TRS504 3.6 20.4 0.9
O1 C:TRS504 3.7 24.3 0.9
OE2 C:GLU145 3.7 17.0 1.0
C C:TRS504 3.8 18.1 0.9
ND1 C:HIS80 4.1 12.3 1.0
CG C:HIS80 4.1 12.6 1.0
CG C:GLU169 4.2 13.2 1.0
CD C:GLU144 4.2 18.1 1.0
CG C:MET113 4.3 12.6 1.0
CB C:ASP112 4.3 14.4 1.0
CD C:GLU145 4.4 17.8 1.0
N C:TRS504 4.4 19.8 0.9
SD C:MET113 4.5 13.8 1.0
CB C:MET113 4.6 12.0 1.0
OE2 C:GLU144 4.6 19.9 1.0
CD C:PRO170 4.6 12.8 1.0
CA C:ASP112 4.6 12.8 1.0
C C:ASP112 4.7 13.4 1.0
OE1 C:GLU145 4.8 17.1 1.0
CB C:GLU169 4.8 12.6 1.0
O C:ASP112 5.0 12.6 1.0
N C:MET113 5.0 12.2 1.0

Zinc binding site 7 out of 10 in 8uw6

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Zinc binding site 7 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:19.6
occ:0.80
 O2 C:TRS504 2.0 12.6 0.9
OE2 C:GLU145 2.0 17.0 1.0
OD2 C:ASP112 2.1 15.9 1.0
NE2 C:HIS355 2.1 17.0 1.0
N C:TRS504 2.2 19.8 0.9
OE1 C:GLU145 2.5 17.1 1.0
CD C:GLU145 2.6 17.8 1.0
C2 C:TRS504 2.9 16.0 0.9
C C:TRS504 2.9 18.1 0.9
CE1 C:HIS355 3.1 17.9 1.0
CG C:ASP112 3.1 15.0 1.0
CD2 C:HIS355 3.2 18.0 1.0
C1 C:TRS504 3.4 20.4 0.9
OD1 C:ASP112 3.4 16.3 1.0
ZN C:ZN501 3.4 14.3 1.0
O C:HOH860 4.0 49.0 1.0
OE1 C:GLU144 4.0 18.0 1.0
O C:HOH768 4.1 14.3 1.0
CG C:GLU145 4.1 15.6 1.0
ND1 C:HIS355 4.2 18.6 1.0
CG C:HIS355 4.3 19.0 1.0
C3 C:TRS504 4.4 21.0 0.9
CB C:ASP112 4.4 14.4 1.0
O1 C:TRS504 4.5 24.3 0.9
NE2 C:HIS80 4.5 11.6 1.0
O C:HOH835 4.7 31.1 1.0
CE1 C:HIS80 4.7 12.1 1.0
O3 C:TRS504 4.7 22.9 0.9
O C:HOH750 4.8 29.1 1.0
CG1 C:VAL84 4.8 16.9 1.0
OE1 C:GLU169 4.8 13.1 1.0
CB C:ALA354 5.0 17.8 1.0

Zinc binding site 8 out of 10 in 8uw6

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Zinc binding site 8 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:26.0
occ:1.00
 O2 D:TRS504 1.8 26.1 0.9
OD1 D:ASP112 2.0 19.8 1.0
NE2 D:HIS80 2.0 24.5 1.0
OE1 D:GLU169 2.1 22.4 1.0
CD D:GLU169 2.7 22.1 1.0
OE2 D:GLU169 2.7 22.6 1.0
CG D:ASP112 2.8 27.0 1.0
C2 D:TRS504 3.0 29.5 0.9
CE1 D:HIS80 3.0 23.3 1.0
CD2 D:HIS80 3.0 21.5 1.0
OD2 D:ASP112 3.1 25.9 1.0
ZN D:ZN502 3.4 26.5 0.8
OE1 D:GLU144 3.4 24.2 1.0
C3 D:TRS504 3.5 32.6 0.9
OE2 D:GLU145 3.7 35.5 1.0
O3 D:TRS504 3.8 36.1 0.9
C D:TRS504 3.8 31.6 0.9
CD D:GLU144 4.1 25.9 1.0
ND1 D:HIS80 4.1 24.1 1.0
CG D:HIS80 4.2 22.8 1.0
CG D:GLU169 4.2 21.5 1.0
CB D:ASP112 4.2 25.7 1.0
CD D:GLU145 4.4 31.6 1.0
N D:TRS504 4.5 27.6 0.9
CG D:MET113 4.5 24.8 1.0
SD D:MET113 4.5 23.7 1.0
OE2 D:GLU144 4.5 27.4 1.0
CB D:MET113 4.6 25.8 1.0
CA D:ASP112 4.6 26.7 1.0
OE1 D:GLU145 4.6 30.5 1.0
C D:ASP112 4.6 25.8 1.0
CD D:PRO170 4.7 28.6 1.0
CB D:GLU169 4.8 22.2 1.0
O D:ASP112 4.8 26.9 1.0

Zinc binding site 9 out of 10 in 8uw6

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Zinc binding site 9 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:26.5
occ:0.75
 OD2 D:ASP112 1.9 25.9 1.0
OE2 D:GLU145 2.1 35.5 1.0
NE2 D:HIS355 2.2 32.3 1.0
N D:TRS504 2.2 27.6 0.9
O2 D:TRS504 2.3 26.1 0.9
OE1 D:GLU145 2.5 30.5 1.0
CD D:GLU145 2.6 31.6 1.0
C2 D:TRS504 2.9 29.5 0.9
C D:TRS504 2.9 31.6 0.9
CE1 D:HIS355 3.0 37.3 1.0
CG D:ASP112 3.1 27.0 1.0
C3 D:TRS504 3.2 32.6 0.9
CD2 D:HIS355 3.3 35.8 1.0
ZN D:ZN501 3.4 26.0 1.0
OD1 D:ASP112 3.7 19.8 1.0
OE1 D:GLU144 4.0 24.2 1.0
O D:HOH637 4.1 25.3 1.0
CG D:GLU145 4.1 30.2 1.0
ND1 D:HIS355 4.2 38.1 1.0
C1 D:TRS504 4.3 31.8 0.9
CG D:HIS355 4.3 38.2 1.0
CB D:ASP112 4.3 25.7 1.0
O3 D:TRS504 4.5 36.1 0.9
NE2 D:HIS80 4.7 24.5 1.0
O D:HOH744 4.7 41.0 1.0
O1 D:TRS504 4.8 32.1 0.9
CE1 D:HIS80 4.8 23.3 1.0
OE1 D:GLU169 4.8 22.4 1.0
CB D:ALA354 4.9 42.4 1.0
CG1 D:VAL84 4.9 30.9 1.0
CD D:GLU144 5.0 25.9 1.0

Zinc binding site 10 out of 10 in 8uw6

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Zinc binding site 10 out of 10 in the Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:43.6
occ:1.00
 NE2 D:HIS378 2.1 64.3 1.0
NE2 D:HIS383 2.3 64.1 1.0
CE1 D:HIS383 2.4 61.7 1.0
CE1 D:HIS378 2.5 59.0 1.0
CD2 D:HIS378 3.3 52.1 1.0
CD2 D:HIS383 3.7 65.3 1.0
ND1 D:HIS378 3.7 59.0 1.0
ND1 D:HIS383 3.8 63.7 1.0
CG D:HIS378 4.1 49.8 1.0
CG D:HIS383 4.4 67.2 1.0
CE3 D:TRP382 4.8 68.5 1.0

Reference:

J.Osipiuk, M.Endres, E.Kelley, D.P.Becker, A.Joachimiak, Center For Structural Biology Of Infectious Diseases (Csbid). Acetylornithine Deacetylase From Escherichia Coli, Di-Zinc Form. To Be Published.
Page generated: Thu Oct 31 12:35:53 2024

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